Operation XML with Roi5D

This page evaluates the "Operation XML element ROIs" use case expressed on the Roi5D Proposals OME-XML-Model-2005-ROI5D page with respect to the Roi5D OME-XML-Model-2005-ROI5D-Detail data model.

Representation

Arbitrary, user-specified (during acquisition) area in 2D (generally some sort of blob), at a given Z plane

This structure can be expressed as a ROI5D hierarchy with SizeC ROI4Ds (each one corresponding to a different C value, to encompass all channels). Since the Operation presumably occurs at a particular time, each ROI4D would be referenced by the same ROI3D (making use of the new many-to-many capabilities), which in turn is referenced by a single ROI2D identifying the Z plane, that is referenced by a single ShapeArea object that ultimately defines the 2D area. Unfortunately, Rectangle, Square, Ellipse and Circle are not sufficient to exactly specify an arbitrary area in 2D — we will need support for BitMasks (which are briefly discussed on the Roi5D page).

Operation to which this area corresponds (e.g., a particular attempt at photobleaching)

This characteristic is represented by a reference within the Operation XML element to the desired Roi5D expressed in XML.Potentially in the future, user-specified enumeration of these areas across multiple Z planes

This scenario can be handled by specifying multiple ROI2D objects, one for each involved Z plane, that are all linked to either the same ShapeArea (for a cylindrical column) or different ShapeAreas (for a true 3D blob). The 3D blob would need to be discretized (sliced into 2D planes) according to the component Z planes.

Specific queries encapsulating the questions

For a given operation, what is the corresponding targeted area?

This query is easy — the Operation has a Shape attribute that references a specific ROI5D, which identifies the targeted area.

For a given area on a specified Z plane, are there any operation ROIs that overlap? (probably less important)

From the list of ROI5Ds linked from Operations, drill down into the ROI5Ds looking for ROI2Ds with matching Z plane.

For a given Z plane, what operations took place?

This query is harder. An approximation is not too difficult: from the operations that took place on that Z plane (see above query), select all ShapeAreas such that the area's bounding rectangle overlaps with the bounding box in X and Y (I can post the math for this if necessary).

If the given area is non-rectangular, or the ShapeArea is nonrectangular, or both, the query becomes more difficult. Different types of shapes require different cases. In the BitMask case, checking for overlap simply entails finding a single pixel in X and Y that is included for both the given area and the operation's ShapeArea. But this test is not cheap if there are many operations to analyze.